DOI: 
https://doi.org/10.5281/zenodo.8192369

#
# Library of functions used for 
# https://ui.adsabs.harvard.edu/abs/2021arXiv210108005J/abstract
# and
# https://ui.adsabs.harvard.edu/abs/2021arXiv210107998J/abstract
# Please cite the former (the 'methods' paper) when using.



Questions? Email:
clancy.w.james@gmail.com


###### External dependencies ########3

Standard Python:
python3
numpy
matpltlib
argparse
os
sys
pickle
time

Specialist modules:
ne2001 (see https://readthedocs.org/projects/ne2001)
FRB (see https://zenodo.org/record/3403651#.YGVnxGQzZKA)


####################### This code #################
Contained herein:

#### Three main programs: ###
(terribly named)

#1: test.py
This program loads survey data from ASKAP and Parkes, and for the best-fit value of parameters, performs several calculations, produces plots, and outputs.
run with python3 test.py

#2: test_errors.py
As above, except it produces plots requiring data from not just the best-fit, but also 90% error ranges of parameters, the best-fit function when forcing n=0, and the best-fit when setting Emin=10^38.5 erg
run with python3 test_errors.py

#3: cube.py
This program is designed to iterate over many possible values of parameters and estimate the likelihoods for each set.
run first with:
	python3 cube.py
then with steering files.


######## library files #########


#4 zdm.py
Class definition containing a grid of p(z,DM) and all the intermediate data and functions required to calculate it

#5 survey.py
Class definition containing FRB survey parameters and related functions

#6 iteration.py
Functions related to maximum likelihood calculations for FRB surveys, and how to iterate these over a grid of values.

#7 cosmology.py
My own dodgy cosmology calculator containing some simple standard cosmological calculations for simplified flat Universe lambda CDM cosmology, and some functions specific for FRBs

#8 beams.py
Functions related to telescope beamshape, including reading beam data

#9 misc_functions.py
Various miscellaneous functions, many of which are deprecated

#10 errors_misc_functions.py
Similar functions to misc_functions.py, but specifically designed to simultaneously plot results from multiple parameter sets - i.e. as required by test_errors.py

#11 pcosmic.py
A library of function to allow the calculation of p(DM_cosmic). This is an implementation of the routines from https://ui.adsabs.harvard.edu/abs/2020Natur.581..391M/abstract
which requires a numerical optimisation to ensure a mean of unity.


######## Cube steering files #########

#12 launch_cube_job.sh
This is designed to send a batch of 'cube.py' jobs to Pawsey's Magnus GPU clusters.

#13 steer_cube.sh
This is the job steering file sent by launch_cube_job.sh that steers
the submission of cube.py jobs to 24 GPUs on a single node.

#14 Cube/all_params.dat
This contains the multi-demensional cube of parameters to be iterated over
by the cube submisson jobs

######## Directories ######

# BeamData
This directory contains numpy data parameterising \Omega(b) - _bins.npy files give the value of b, _hist.npy files the corresponding values of \Omega. Those in log-space should be named as such, but beams.py tests this. Gaussian beams can also be generated in beams.py

# Surveys
Directory containing survey information, specifying details of ASKAP and Parkes FRB surveys. These get read by the survey class defined in surveys.py

# Pickle
This directory is for saving data for efficient re-use. In particular, calculating a p(z,dm) grid for a single survey takes more than a minute on a single processor, while many plotting routines by default save data here to allow rapid recalculation.

# Cube
Directory containing inputs and outputs for cube.py

# Plots
Directory for all plots generated by test.py

# ErrorPlots
Directory for all plots generated by test_errors.py

# GridData
Save directory for grids of the intrinsic p(DM_cosmic | z) distribution